Re: [ccp4bb]: "locked" translation search

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***

Risal wrote:
> 
> ***  For details on how to be removed from this list visit the  ***
> ***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***
> 
> Dear all,
> 
>         I have a P212121 dataset with four molecules in the asu. I am
> trying to place my  model molecules in the cell with Amore. But the
> correlation coefficients (and R factors) are poor for both rotation and
> translation search hits (no peak really stands out above background). I
> used "rfcorr" to weed out poor/crystallographic hits in the cross-rotation
> search so that I could work with a smaller set of cross-rotation hits that
> I could visually inspect with a display program. I *think* I have one
> cross-rotation peak (hit) that I can use. This peak is related by a
> twofold to another (theta, phi, chi= 2, 23, 180).
> 
>         When I do a straightforward translation search with my "best"
> hits, I get two molecules which bump into one another. This leads me to
> believe that things are going wrong during the translation search (due to
> the poor quality of peaks.)
> 
>         Can Amore to do a 'locked' translation search so that it
> acknowleges my two-fold while doing the search (and therefore increase
> signal-to-noise)? Any help will be greatly appreciated.
> 
> Dipesh Risal
> University of Rochester
> 


 First of all, have you done a native patterson. With 4 molecules in the
asymmetric unit it is likely that there wll be some alignment. If you
get a peak with either x or y or z as 1/2 then you must consider whether
your space group could be incorrect - a pseudo-translation of 1/2 will
generate absences along that axis. 


 
(in fact if you are using ccp4i this is the first instruction on the
task window..)

Secondly, does your model form a tetramer or a dimer? If so it is often
best to search with that rather than single molecules. 
Thirdly if the pseudo symmetry aligns near to a crystallographic axis
the rotation may be disguised.

 But to answer your question, Amore can do a locked rotation function,
but it requires that you get the rotation function sorted.
 And you can use MOLREP which is more automated.

 Eleanor
-- 
------------------------------------------------------------------
Eleanor J.Dodson, Chemistry Department, University of York, U.K.
Tel: Home +44 (1904) 42 44 49, work:  +44 (1904) 43 25 65
------------------------------------------------------------------